1jke - Revision history

OCA at 07:40, 7 February 2024

OCA — Wed, 07 Feb 2024 07:40:09 GMT

←Older revision		Revision as of 07:40, 7 February 2024
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	<StructureSection load='1jke' size='340' side='right'caption='[[1jke]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='1jke' size='340' side='right'caption='[[1jke]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jke]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1JKE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jke]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JKE FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.55Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>YIHZ or B3887 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1jke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jke OCA], [~~http~~://pdbe.org/1jke PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1jke RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1jke PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1jke ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1jke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jke OCA], [https://pdbe.org/1jke PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jke RCSB], [https://www.ebi.ac.uk/pdbsum/1jke PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jke ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DTD_ECOLI DTD_ECOLI]] Hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). Could be a defense mechanism against a harmful effect of D-tyrosine. Can also cleave D-aspartyl-tRNA(Asp) and D-tryptophanyl-tRNA(Trp).	+	[https://www.uniprot.org/uniprot/DTD_ECOLI DTD_ECOLI] Hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). Could be a defense mechanism against a harmful effect of D-tyrosine. Can also cleave D-aspartyl-tRNA(Asp) and D-tryptophanyl-tRNA(Trp).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1jke ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1jke ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Cell growth inhibition by several d-amino acids can be explained by an in vivo production of d-aminoacyl-tRNA molecules. Escherichia coli and yeast cells express an enzyme, d-Tyr-tRNA(Tyr) deacylase, capable of recycling such d-aminoacyl-tRNA molecules into free tRNA and d-amino acid. Accordingly, upon inactivation of the genes of the above deacylases, the toxicity of d-amino acids increases. Orthologs of the deacylase are found in many cells. In this study, the crystallographic structure of dimeric E. coli d-Tyr-tRNA(Tyr) deacylase at 1.55 A resolution is reported. The structure corresponds to a beta-barrel closed on one side by a beta-sheet lid. This barrel results from the assembly of the two subunits. Analysis of the structure in relation with sequence homologies in the orthologous family suggests the location of the active sites at the carboxy end of the beta-strands. The solved structure markedly differs from those of all other documented tRNA-dependent hydrolases.
-
-	Structure of crystalline D-Tyr-tRNA(Tyr) deacylase. A representative of a new class of tRNA-dependent hydrolases.,Ferri-Fioni ML, Schmitt E, Soutourina J, Plateau P, Mechulam Y, Blanquet S J Biol Chem. 2001 Dec 14;276(50):47285-90. Epub 2001 Sep 21. PMID:11568181<ref>PMID:11568181</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1jke" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Blanquet, S]]	+	[[Category: Blanquet S]]
-	[[Category: Ferri-Fioni~~, M L~~]]	+	[[Category: Ferri-Fioni ML]]
-	[[Category: Mechulam, Y]]	+	[[Category: Mechulam Y]]
-	[[Category: Plateau, P]]	+	[[Category: Plateau P]]
-	[[Category: Schmitt, E]]	+	[[Category: Schmitt E]]
-	[[Category: Soutourina, J]]	+	[[Category: Soutourina J]]
-	~~[[Category: Beta-alpha-barrel]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:32, 25 November 2020

OCA — Wed, 25 Nov 2020 07:32:43 GMT

←Older revision		Revision as of 07:32, 25 November 2020
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	==D-Tyr tRNATyr deacylase from Escherichia coli==		==D-Tyr tRNATyr deacylase from Escherichia coli==
-	<StructureSection load='1jke' size='340' side='right' caption='[[1jke]], [[Resolution\|resolution]] 1.55Å' scene=''>	+	<StructureSection load='1jke' size='340' side='right'caption='[[1jke]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jke]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKE OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1JKE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jke]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1JKE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YIHZ or B3887 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YIHZ or B3887 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1jke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jke OCA], [http://pdbe.org/1jke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jke RCSB], [http://www.ebi.ac.uk/pdbsum/1jke PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jke ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1jke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jke OCA], [http://pdbe.org/1jke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jke RCSB], [http://www.ebi.ac.uk/pdbsum/1jke PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jke ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Blanquet, S]]		[[Category: Blanquet, S]]
	[[Category: Ferri-Fioni, M L]]		[[Category: Ferri-Fioni, M L]]

OCA at 09:01, 17 January 2018

OCA — Wed, 17 Jan 2018 09:01:36 GMT

←Older revision		Revision as of 09:01, 17 January 2018
Line 1:		Line 1:
		+
	==D-Tyr tRNATyr deacylase from Escherichia coli==		==D-Tyr tRNATyr deacylase from Escherichia coli==
	<StructureSection load='1jke' size='340' side='right' caption='[[1jke]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='1jke' size='340' side='right' caption='[[1jke]], [[Resolution\|resolution]] 1.55Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YIHZ or B3887 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YIHZ or B3887 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jke OCA], [http://pdbe.org/1jke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jke RCSB], [http://www.ebi.ac.uk/pdbsum/1jke PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jke OCA], [http://pdbe.org/1jke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jke RCSB], [http://www.ebi.ac.uk/pdbsum/1jke PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jke ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jk/1jke_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jk/1jke_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 03:00, 9 February 2016

OCA — Tue, 09 Feb 2016 03:00:41 GMT

←Older revision		Revision as of 03:00, 9 February 2016
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1jke ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:57, 10 September 2015

OCA — Thu, 10 Sep 2015 17:57:46 GMT

←Older revision		Revision as of 17:57, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1jke' size='340' side='right' caption='[[1jke]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='1jke' size='340' side='right' caption='[[1jke]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jke]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JKE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jke]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JKE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YIHZ or B3887 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YIHZ or B3887 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jke OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jke RCSB], [http://www.ebi.ac.uk/pdbsum/1jke PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jke OCA], [http://pdbe.org/1jke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jke RCSB], [http://www.ebi.ac.uk/pdbsum/1jke PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1jke" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Blanquet, S]]		[[Category: Blanquet, S]]
	[[Category: Ferri-Fioni, M L]]		[[Category: Ferri-Fioni, M L]]

OCA at 03:57, 25 December 2014

OCA — Thu, 25 Dec 2014 03:57:00 GMT

←Older revision		Revision as of 03:57, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1jke]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JKE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1jke]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JKE FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YIHZ or B3887 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YIHZ or B3887 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jke OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jke RCSB], [http://www.ebi.ac.uk/pdbsum/1jke PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jke OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jke RCSB], [http://www.ebi.ac.uk/pdbsum/1jke PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DTD_ECOLI DTD_ECOLI]] Hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). Could be a defense mechanism against a harmful effect of D-tyrosine. Can also cleave D-aspartyl-tRNA(Asp) and D-tryptophanyl-tRNA(Trp).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Blanquet, S.]]	+	[[Category: Blanquet, S]]
-	[[Category: Ferri-Fioni, M L.]]	+	[[Category: Ferri-Fioni, M L]]
-	[[Category: Mechulam, Y.]]	+	[[Category: Mechulam, Y]]
-	[[Category: Plateau, P.]]	+	[[Category: Plateau, P]]
-	[[Category: Schmitt, E.]]	+	[[Category: Schmitt, E]]
-	[[Category: Soutourina, J.]]	+	[[Category: Soutourina, J]]
	[[Category: Beta-alpha-barrel]]		[[Category: Beta-alpha-barrel]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 09:27, 3 October 2014

OCA — Fri, 03 Oct 2014 09:27:35 GMT

←Older revision		Revision as of 09:27, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1jke\| PDB~~=1jke \| ~~SCENE~~= }}	+	==D-Tyr tRNATyr deacylase from Escherichia coli==
-	===~~D-Tyr tRNATyr deacylase~~ from Escherichia coli===	+	<StructureSection load='1jke' size='340' side='right' caption='[[1jke]], [[Resolution\|resolution]] 1.55Å' scene=''>
-	~~{{ABSTRACT_PUBMED_11568181}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1jke]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JKE FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YIHZ or B3887 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jke OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jke RCSB], [http://www.ebi.ac.uk/pdbsum/1jke PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jk/1jke_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cell growth inhibition by several d-amino acids can be explained by an in vivo production of d-aminoacyl-tRNA molecules. Escherichia coli and yeast cells express an enzyme, d-Tyr-tRNA(Tyr) deacylase, capable of recycling such d-aminoacyl-tRNA molecules into free tRNA and d-amino acid. Accordingly, upon inactivation of the genes of the above deacylases, the toxicity of d-amino acids increases. Orthologs of the deacylase are found in many cells. In this study, the crystallographic structure of dimeric E. coli d-Tyr-tRNA(Tyr) deacylase at 1.55 A resolution is reported. The structure corresponds to a beta-barrel closed on one side by a beta-sheet lid. This barrel results from the assembly of the two subunits. Analysis of the structure in relation with sequence homologies in the orthologous family suggests the location of the active sites at the carboxy end of the beta-strands. The solved structure markedly differs from those of all other documented tRNA-dependent hydrolases.

-	~~==Function==~~	+	Structure of crystalline D-Tyr-tRNA(Tyr) deacylase. A representative of a new class of tRNA-dependent hydrolases.,Ferri-Fioni ML, Schmitt E, Soutourina J, Plateau P, Mechulam Y, Blanquet S J Biol Chem. 2001 Dec 14;276(50):47285-90. Epub 2001 Sep 21. PMID:11568181<ref>PMID:11568181</ref>
-	~~[[http://www.uniprot.org/uniprot/DTD_ECOLI DTD_ECOLI]] Hydrolyzes~~ D-~~tyrosyl-tRNA(~~Tyr~~) into D~~-~~tyrosine and free~~ tRNA(Tyr). ~~Could be~~ a ~~defense mechanism against a harmful effect~~ of D-~~tyrosine~~. ~~Can also cleave D~~-~~aspartyl-tRNA~~(~~Asp~~) ~~and D~~-~~tryptophanyl-tRNA(Trp)~~.	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[1jke]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1JKE OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:011568181</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Blanquet, S.]]		[[Category: Blanquet, S.]]

OCA at 10:32, 16 April 2014

OCA — Wed, 16 Apr 2014 10:32:57 GMT

←Older revision		Revision as of 10:32, 16 April 2014
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-	[[Image:1jke.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_1jke", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1jke\| PDB=1jke \| SCENE= }}		{{STRUCTURE_1jke\| PDB=1jke \| SCENE= }}
-
	===D-Tyr tRNATyr deacylase from Escherichia coli===		===D-Tyr tRNATyr deacylase from Escherichia coli===
		+	{{ABSTRACT_PUBMED_11568181}}

-		+	==Function==
-	~~<!--~~	+	[[http://www.uniprot.org/uniprot/DTD_ECOLI DTD_ECOLI]] Hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr). Could be a defense mechanism against a harmful effect of D-tyrosine. Can also cleave D-aspartyl-tRNA(Asp) and D-tryptophanyl-tRNA(Trp).
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_11568181}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov~~)~~, where 11568181 is the PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_11568181}}~~	+

	==About this Structure==		==About this Structure==
Line 22:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:011568181</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011568181</ref><references group="xtra"/><references/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Blanquet, S.]]		[[Category: Blanquet, S.]]

OCA: Protected "1jke" [edit=sysop:move=sysop]

OCA — Wed, 16 Nov 2011 10:41:52 GMT

Protected "1jke" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:41, 16 November 2011

OCA at 10:41, 16 November 2011

OCA — Wed, 16 Nov 2011 10:41:50 GMT

←Older revision		Revision as of 10:41, 16 November 2011
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-	{{Seed}}
	[[Image:1jke.png\|left\|200px]]		[[Image:1jke.png\|left\|200px]]

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	==About this Structure==		==About this Structure==
-	~~1JKE~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKE OCA].	+	[[1jke]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKE OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11568181~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011568181</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Blanquet, S.]]		[[Category: Blanquet, S.]]
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	[[Category: Soutourina, J.]]		[[Category: Soutourina, J.]]
	[[Category: Beta-alpha-barrel]]		[[Category: Beta-alpha-barrel]]
-		+	[[Category: Hydrolase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 05:55:53 2009''~~	+